"We still haven't got Wes Morgan or Papy Mendy. How long they'll be out for, I can't put a time frame on it," Shakespeare told a news conference.
"Wes has been out on the grass in his boots, Papy hasn't. He'll see another specialist. To ask Wes to come back for a game of that magnitude (Atletico Madrid) would be a huge ask. I'd want him to do a few days training."
Shakespeare, who took over from Claudio Ranieri in February, has steered Leicester away from the relegation zone with five consecutive league victories.
The team are currently 11th in the domestic standings and will play the first leg of their Champions League quarter-final on Wednesday, but Shakespeare said he would not field a weakened team against Everton.
"There hasn't been any Champions League talk. It hasn't been banned, it's just all about keeping the run going against Everton. I'll assess the squad over next 24 hours and pick a team that can win at Everton. Focus on Everton, not Madrid."
Everton, who are seventh, beat Leicester 3-1 in the reverse fixture in December.
(Reporting by Hardik Vyas in Bengaluru; editing by Mark Heinrich)
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